Second Chance
by InfiniteWings
Summary: A different world, a different story. It started out the same, but when some small things are changed, the outcome can be very different. Gendo, Naoko and Ritsuko work to defend the world against Angels and prevent Instrumentality, which was presented by Yui. Shinji works as a pilot along with Rei, Kaworu, and soon, some others. Small differences, large changes.
1. Chapter 1

Second chance

Disclaimer: I don't own Evangelion. Anno does.

Shinji Ikari stood before the telephone booth. The phone wasn't working, and the woman hasn't arrived yet. He stared at the postcard again. He wondered. Suddenly, a slab of Stone fell next to him. He turned, and saw a gigantic monster walking through the streets, unaffected by the huge amount of firepower sent at its direction. Gasping, he ran the other way, then a blue sedan stopped before him.

"Come on in!" The purple haired woman beckons him in, smiling. "Sorry to have kept you waiting!"

He entered the car. The woman took off her sunglasses. "I'm Misato Katsuragi," she said.

He steps onto the bridge as the lights turn on before him. He steps backwards as he soon as he saw the monstrosity before him.

"A...a…"

"This is the multi-purpose bio mechanical humanoid fighting machine Evangelion." Said Misato, as she insisted him call her. "This is your father's work."

"Father…"

"Shinji." Said Gendo Ikari, who stood behind a piece of glass. "You will pilot it to fight the Angel."

Shinji almost fell backwards in shock. He wasn't expecting this at all.

"It's been three years, and this is what you ask?"

"Will you pilot it or not? If you will, then get in. If not, then get out of my sight."

"I didn't come here for this!"

Gendo inwardly sighs. He'll have bring out the clone. He always hated the way he had to portray his son, just to fool the committee - a total wimp.

"Ritsuko," he called through the PA system. "Bring Rei. The spare, third child, proved useless."

Obviously he didn't need me… there was always someone else, wasn't there?

"But, commander, Rei is in no shape to fight!"

"She isn't dead."

"How can you?" A new voice, filled with anger, and was it? A hint of concern, joined the conversation. "If you send her out, she'll die!"

"That is not my fault, fifth child. Or would you like to pilot instead?"

"You know obviously that Yui Ikari would never accept me, Gendo Ikari. Or would she, but you didn't let her, because you know you can't use me?"

"Do not mention her name." The face of the commander reddens. As all know, the fifth was the only one who the commander somehow respected, ( or was it fear, as some speculated? ), as if he was of the same rank as he is. Strangely though, he was also the only one Rei Ayanami, first child, is close to. Few knew the truth of who he was, as he had joined them one day, all records erased, without any hint as to how he came to this world except that his birthday was the day of Second Impact.

"You said the spare would work. The committee will not forgive you if the scenario fails now!"

"All of this is no matter. Rei shall pilot, as the third child refuses to."

"Then I will go with her! Rei will be able to help me sync, and with me she stands a better chance of survival."

"As you wish. Though, the Angel is coming soon, can you hurry?" The hidden smile often on Gendo's face, however, had disappeared as the boy mentions the committee. It was hard to keep them off his back, with him there always watching him. And he can't really get him removed yet, since Rei is close to him. He wondered how this clone of a human had been able to get close to Rei, when even he himself couldn't. Save those thoughts, he told himself. I won't let you win, Yui.

Just as they finished speaking, Shinji turns and saw the doctor, referred to just now as Ritsuko, push a hospital bed on a bridge. Lying on it was a blue haired, red eyed albino girl. She had bandages all over her body, as if she was a fragile doll, easy to be broken. And beside her, holding her hand and whispering words of comfort to her, was a boy who looked eerily similar to her, except that he had grey hair. Seeing Shinji standing there, staring, he glared, accusation clear in his eyes.

 _I can't do it… I just can't. I haven't even seen this thing at all!_

Suddenly, the whole place shook, causing the bed to turn, and the girl, Rei, fell off the bed and into the boy's arms. Holding her up, he turns and looked at Shinji. But this time, those eyes were almost pleading.

"I'll do it!" Shinji cries out. "I'll pilot the Evangelion!"

The boy relaxed visibly. Placing Rei gently onto the bed and giving Ritsuko some gentle words, he walks over to Shinji.

"My name is Kaworu Nagisa. I am the fifth child, pilot of Unit Beta, which is currently being built. I will go into the entry plug with you, in order to help you defeat the Angel. However, it is you who will go through the mental process of syncing with the soul. I can only work as the mind for you. If all is clear, follow me to the entry plug."

Shinji follows him, and wonders how he can be that assertive, even to his father.

"Are you sure you want to do this?" Ritsuko asked the boy, concern and could it be… motherly love? in her eyes.

"Yes. Shinji will need my help. And this is the only way so that Rei wouldn't have to fight, at least until they finish Unit Beta. Is there any news on when it's going to be done?"

"I believe not. However, the second child will come to Japan soon, along with Unit 2, if the committee allows it. And your sister also, possibly." Ritsuko frowned. The committee… this was the only reason she hadn't adopted the boy as her own. He was the committee's, and she couldn't really do much. As much as she loved him, he was not someone who she can trust with all Gendo's secrets, if he didn't know them already.

 _It was all because of Yui…_

The commander's dead wife. And the reason why she still pretends to have an infatuation with Gendo. All to fool the committee. Yui tried to kill her mother, and escaped into the Evangelion, while her mother, shocked by the attempt, left for Nerv-Berlin to cool down, and almost got killed in the flight. All that contributed to her mother now in a coma, despite still being alive due to Kaworu. And Rei… she couldn't forget the truth behind the girl, despite the fact Kaworu and her both know that it wasn't her who tried to kill her mother, and it was Yui who planned it all.

But she cared for both of them, really. Two children who were clones of their makers, containing souls of power like nothing else. Two souls meant for each other, searching for a way to escape the plans that seemed set into stone. She maintained the other clones, and secretly saved their memories even though she was told not to. But they were like her children. And she found in them a way to redeem herself from what she did years ago.

"Evangelion shogouki, start up!"


	2. Chapter 2

Chapter 2: Mother and Father

The two of them sat in the entry plug, with Shinji tense and nervous, while Kaworu simply leaned back and closed his eyes. If only Yui never made such a mess for us to clean up. But then again, I wouldn't have been able to enter this timeline without it. Suddenly, the plug was filling with an orange liquid. Shocked, Shinji cried out.

"It's only the LCL. It is what allows you to sync with the Evangelion. When you have enough of it in your lungs, you will be able to breathe in it. Just relax, Shinji Ikari,"

"You won't be able to help if you don't calm down."

And then, the image of Yui Ikari appears. She was like a phantom, floating out towards them. Embracing him, Shinji could find no words, simply warm in his mother's arms. However, he did not spot the bright crimson in his mother's eyes, nor the sinister way she glared at Kaworu.

"Get out. I only want my son here."

"He can't do it yet. He's not strong enough. Aren't you a mother? Aren't you supposed to protect your son? This isn't how!"

"l'll protect him. You don't need to be here."

"Don't you dare. I am better at syncing. Just this once! Do you need your son to be so broken, just for your twisted plans? Naoko didn't deserve that. And now Rei suffers because of what you've done."

To that extent, she actually looked guilty while Shinji curls in her embrace. "Her daughter tried to kill my son! What else do you think I should do? I can't let that happen!"

"Then let me protect your son this time! I failed him last time. I won't this time! You were the one who killed me, not him, I know."

"Only this once." She gave one last glance at her son, then disappeared. Kaworu felt her presence letting him in, and smiles. This time, he won't fail. Rei needs him.

Seemingly more calm after being in his mother's embrace, Shinji placed his hands onto the controls, as the Unit slowly progresses towards the lift. As the bridge bunnies clicked a few keys, the Unit blasted off. Going upwards, Shinji gasped in shock at the speed, while Kaworu just waits.

The Angel stood on the far end of the street, and sees the Eva. Shinji's hands began to shake, though he didn't let go of the controls.

I mustn't run away. For all of them, I mustn't run away...

"Shinji, thank you for doing the hardest bit for me. You don't need to worry now. I will defend you this time." _Thank you, Yui, you too._ Kaworu whispers, then took Shinji's place. Taking the progressive knife from the shoulder pylons, he -and the Eva, of course, pounced.

The battle was quick. It didn't take long to finish off the Angel, as he pretty much plunged the knife into the core as soon as possible, effective and mercilessly killing it.

Shinji, however, will never forget the haunted look on Kaworu's face, when the Angel had seemed to make a strange sound. It was as if there was something he heard, something that makes him remember things he wished to forget.

 _Kaworu knocks Sachiel to the ground, with Sachiel struggling feebly underneath the Eva. He eyes hard with determination, the progressive knife in his hand ready, he looks Sachiel in the eye._

 _'Any last words, Sachiel?' He spoke, the voice of an Angel rumbling in Sachiel's mind._

 _'You betray our kind, Tabris! Why do you do this to us? The power of Adam was given to you, yet you ally yourself with Lilin. What do you do this for?'_

 _'Because of love.'_

 _He plunges the progressive knife in, cracking the core. But he remembers. All the times in which he failed, in which he pays the price. His brothers and sisters, not ever knowing the beauty of Lilin, never understood. All he received, was punishment._

When they brought the stretchers to their entry plug, Kaworu shook his head. "I wasn't injured," he said. "Neither of us were. But you should find Captain Katsuragi. She is probably going to be the best person able to comfort him now.

Nodding as they walked away, the medics left. The two boys then saw Dr Akagi and Captain Katsuragi walking over.

"You did well, Shinji-kun." The Captain smiled warmly at him.

"But I didn't do anything!"

"No, Shinji. That is incorrect. Without your presence, Kaworu would not have been able to sync with the Eva, and the battle would not have been won." Ritsuko, being the scientist, replied.

"We need you, Shinji-kun." Kaworu added.

 _I am… needed? Can this be true?_

They then walked towards the elevator to his father's office, as they needed to know the details on where Shinji will live, and report their status. He didn't realise Misato held his hand, until he realises how sweaty it was.

Entering the office, the first thing Shinji noticed is the patterns on the ceiling and the floor. Having done a bit of studies himself, he realises what it was.

"The sephiroth tree, or tree of life in Kabbalistic beliefs."

"Correct."

Gendo Ikari, supreme commander of Nerv, actually smiles. "How are you, Shinji?"

 _He cares! He cares if I pilot the Eva. Then I must do it._

"I am fine, Father."

"That is good. With many things taken into account, since I am quite busy, you cannot live with me. However, you shall live with Captain Katsuragi."

"Oh sure! You'll love my place. Come along!" She pulls Shinji closer to her, a warm smile on her face.

She seems so welcome. Am I really… cared about?

"Yes." He replied.

"Any questions?"

All of them shook their heads.

"Then all of you are dismissed." Gendo said, his normal look returning. But before they walk into the elevator, he calls out.

"Shinji."

"Yes, Father?"

"You did well. I am proud of you, Shinji."

And after three years since his mother's disappearance, this was the first time he sees him smile.

Watching the scenario play out from the side, Kaworu narrows his eyes. _Can I trust Gendo Ikari? He surely doesn't trust me, but what is his agenda really? What does he get out of this? Seele is bearing down his back, but I know there must be more to this. I must figure out his plans. I can't fail._


	3. Chapter 3

Chapter 3: The mother inside the woman who is a scientist

Dr Ritsuko Akagi sits at her computer, carefully checking the Magi records. According to it, there was an irregularity in the syncing process with Unit 01, and that Kaworu had synced with it 35 seconds later than expected of a normal sync.

 _Why did you do what you did, Yui? Was it all for your son? Is the mother inside you so twisted, you believe this is good for him?_

A mother… she never had the chance to make herself one. Though, she would admit, she always thought herself the mother of Rei and Kaworu. Those children, she thought. They never had a chance at a normal life.

Checking that the data was correct, she moved on to the paperwork. These days, there might be a chance that she'll just get tired of it all and resign, leaving mankind's fate to itself. Then again, she would never do that to the children. They needed her.

Sighing, she lights a cigarette. A report on the status of the Eva was supposed to be done by tomorrow. Maya had been of great help, as usual. Her thoughts wandered towards her cat. She wondered how it was doing. And her mother… she wished there could be a chance that she'll wake from her coma. Life wasn't easy.

To her surprise, the door opened quietly. Standing there was Kaworu, a look of concern on his face.

"You should go home and rest, Ritsuko-san." He whispers softly. "Too much work isn't healthy. Nor is that cigarette."

"It's fine, Kaworu. I think there's just a little more I need to do. Gendo needs the report tomorrow."

"He's being too hard on you."

"It's just duty. Mind if you brew me a cup of coffee? You can go home first after that. It's not good for children to sleep late. Rei probably went home already."

"I'm here too." She said suddenly.

"Ritsuko-san, just rest. You're getting tired and you need sleep, even if we don't."

"I guess so then." She replied, yawning as she realised what time it was. "Oh dear, it's three in the morning already?" As the children dragged her into the car, driving themselves- she didn't know how they pulled it off, but they always did- she fell asleep to the dialogue of the children's quiet whispers.

 _She looks around her. She was in that same lab again. Watching from the window, she saw how Gendo tries to persuade Yui to give up on the Human Instrumentality Project, how it was unrealistic and ridiculous. Her own mother joins in, and she saw that hint of jealousy in Yui's eyes, that Gendo, though married to her, still has eyes for another woman._

 _It was still the days of Gehirn, as they were working on the Evas. That day, Yui had walked in, an infant in her arms, a little girl holding the other._

 _"These are my children, Shinji Ikari, and Ayanami Rei, who is artificially made with my own and Lilith's genes." She had told Naoko proudly. She was horrified then. The girl said nothing, only doing everything Yui asked, from the most trivial tasks to her last, ordered by Yui._

 _At then, she was worried for her mother. That she will lose herself if she doesn't get Gendo. And Gendo did care for Naoko, actually. And all that stood in the way was Yui. And her son._

 _He was the only true proof. The person who really could stop it from being real._

 _That night, she sneaked into Yui's office, and found baby Shinji lying there. So innocent, so pure. But this was her chance. So she placed her hands on his throat, and squeezed._

 _Yui walked in right then, Rei trailing behind her. She was horrified then, of what she would do. She was a mother, after all._

 _What she did, was truly twisted indeed._

 _"Kill the doctor Naoko Akagi." Yui had told Rei._

 _She had gasped in horror, preparing to run out to save her mother, when Yui stops her with her handgun._

 _"This is the price you pay for trying to kill my son!" She had screamed._

 _After what had seemed like forever, there was a loud gunshot._

 _"You may go now," Yui had said then, a twisted and cruel smile playing on her lips._

 _She rushed out, all the way to Naoko's office. There, arms wrapped around herself, was a very shaken Naoko, and a fourteen year old, grey haired, crimson eyed albino boy who stood over the dead body of Rei I._

 _She was very shaken then too, as the boy, Kaworu, as he calls himself, explains the situation with Rei, and himself. Of what they are. Naoko had fainted, too shaken by all that's happened, as she herself and Kaworu went to Yui's office._

 _At first she was smirking, then she realised that Naoko was probably still alive. With no other way to escape, she jumps into the entry plug of Unit 01, saying that they will pay in the future. Kaworu then left, saying they will meet again, and joins her mother on the plane to Berlin. And soon after, her mother falls into a coma, she discovers the Rei clones, and Gehirn reforms into Nerv._

 _All was wrong. Just because of her own stupidity, trying to kill Shinji, caused Mother to fall into a coma._

 _"It wasn't your fault." Kaworu whispers in her dream._

Suddenly, she realised that she had no idea how Kaworu knew Yui's sudden attempt to kill Naoko, and how he arrived in time. But then, as she blinked, facing the ceiling of her room, the dream faded. She knows she will not make that mistake again.

 _A mother, a woman, a scientist. How do I be any of them, without sacrificing another? That was the mistakes both of them made. I can't fail my children._

 _My children,_ she realised. _I called them that in my mind._

Stepping out into the light, she sees the breakfast already made for her. Rei stood there, a shy smile suggesting that she made it. Calm down, she told herself. This is not that Rei. This is not Yui's Rei. This is a Rei who will get to choose. One who can be free from Yui.

As she placed the rice dumpling within her mouth, she noticed how wonderfully delicious it was.

"It tastes great, Rei."

And then she hugs her. Not just loosely, as expected of any mother. But tight and heartwarming, not letting go.


	4. Chapter 4

Chapter 4: The woman who is a scientist, once had a mother

Ritsuko walks into Gendo's office. He sat, and unlike his usual self, in a relaxed way.

"How's the report?"

"Here." She said, laying it out before him. "It surprises me you can hold off the committee, faking your long gone love for Yui, and your lack of attention to your son."

"I do owe Naoko a lot."

"Actually, in a way, I'm your daughter, you know. The committee is really dumb to think I'm actually infatuated with you."

"The committee can believe whatever it wants. Though, shouldn't you keep some distance from their boy?"

"Kaworu is like my child to me. He saved my mother."

"Still, I can't trust him. Yet. Worst case scenario, we might even need to remove him."

"I don't think he's all for the committee. They weren't very kind to him. Besides, he cares about me too."

"Well, at least don't spill your guts. The committee can't know that we are going to stop their plans. Who knows what they'll do to us."

"I won't. But you've got to trust him more. He and Rei make a good pair, don't you think?"

"He's technically your son, while Rei's technically my daughter."

"You're so old fashioned. I care for Rei, so she's my daughter too."

"At least they trust you. I don't know how to reach my son."

"A good way of connecting to Shinji is to spend time with him. Show him you care."

"Rits!" Misato called. "I have important news for you."

"What is it? You rarely look that concerned."

"They're sending in Unit 02 and Unit Beta from Berlin. Along with the pilot. Unit Alpha didn't work out, as you know. Don't tell the boy too soon. He will be distraught. Somehow, they've finally decided that we'll need them more. Also, there's something you should know…"

"Just say it."

"Your mother. They're sending her over. Her mental state's erratic, and they think she's not going to have much time left. So they want you to be able to see her one last time."

"I see." She says curtly, walking away, hiding that tear that slides down her cheek.

 _Mother, even Kaworu couldn't save you, could he? He only delayed the inevitable. But you tried so hard… I thought you would wake up._

"Sempai!" Maya called out.

"Yes, Maya?"

"Something irregular is going on in the Magi- Casper kept showing a file that requires a passcode to unlock. And we couldn't do anything to override it."

"I'll check it, Maya. Thanks for telling me." She said, the messages Misato and Maya brought her on her mind.

 _Mother… is there something you wish to tell me before you go?_

She stared at her computer screen.

MAGI CASPER ENCRIPTED FILE: NAOKO AKAGI

PASSCODE REQUIRED

"Gehirn" She typed the word in. That was obviously the answer, as it was the last word she said before she fell into a coma, the others told her.

ACCESS ALLOWED

She sighed. Opening the file, she reads out the contents to herself.

 _Dear Ritsuko,_

 _If you're reading this, then Kaworu must have alerted me that the Angels have started coming, causing that I will be brought back to Japan. Do not worry, I won't be dying yet. Here, as I am on my way to you, I shall explain why I left you, in a coma._

 _Before the incident with Yui, I was in a way, confused. I didn't really understand how to balance out between my duty as a mother, my work as a scientist, and my heart as a woman. I shouldn't have went that far with Gendo, even if he did feel something for me, perhaps. But then, it's too late now, there isn't a way to change what's in the past. But then, mankind's future depends on us, so there are things we must do._

 _Yui had presented to the committee, before everything, a plan. The Human Instrumentality Project, as you know. But what you probably didn't know, was that she prepared it for her son. She was going to give birth to Shinji, and she thought with the world in that state, she could make him into a God, letting him choose his world, free from hurt and pain._

 _She forgets that hurt and pain are both lessons that one must learn in life, that it is actually necessary for him to learn those things. However, she neglects that, wishing to give him a perfect world, and thus we have the Human Instrumentality Project. Gendo tries to stop her, but naturally he fails. Seeking affirmation that he is right, I came into question. You know what happened later on, but I just wanted to make sure you know._

 _However, I didn't fall into a coma because of an accident on the plane. I knew it was the only way to placate Yui, so I asked Kaworu to do it. You have to trust him. He's our only chance. As to why, you'll have to ask him himself. That is his to tell. He's like a grandson to me. He speaks well of you, and how you helped Rei. But anyways, I believed it was the only way to protect you from Yui, as she took control of Unit 01. I am sorry for leaving you alone all these years, but I'm sure you found something by yourself, didn't you?_

 _Well now that the Angels have come, it is necessary that I am alive. I shall awaken from my slumber. Yui would not be able to harm me, because of her son's presence. Don't hurt him. He doesn't know anything of what happened in the past, and he is innocent. What is in the past is gone, and if we all live through this, maybe Gendo and I can find something. But now, we must be careful. We can't afford to lose._

 _I look forward to seeing you again, and I hope you forgive me for my absence all these years._

 _From your mother,_

 _Naoko Akagi_

 _P.S. This file will be deleted by the time you close it._

Memorising every word of the letter, Ritsuko wipes away her tears. A small smile forms.

"Mother," she whispers to Casper.

"Of course I forgive you. It was all for me, wasn't it?"


	5. Chapter 5

Chapter 5: Truth act I

Gendo Ikari sat on his chair in his office, musing. He wondered how his son was faring. Checking his schedule, he realised that there was nothing for him to do today. How surprising. Perhaps he should visit his son. He would probably appreciate that. He had neglected him for too long. They tell him they're shipping Naoko back to Japan. _At last_ , he thought. It has been far too long. _I wonder what Ritsuko thinks. She would probably be surprised. I still cannot believe or understand your actions then, Yui._

He stood up, and hands behind him, he entered the elevator.

Shinji Ikari was inside the kitchen of Misato's home, making breakfast. He had spent the recent few days trying to adjust, finding Misato a very different person than how he expected. The sole fact that her refrigerator was filled with cans of beer says a lot about a person, though it does not necessarily show that she was a bad person.

 _Is Misato Katsuragi a nice person? I don't understand…_

He smiled, however, as he finishes the rice roll. There seemed to be some extra, so he kept them as he places two plates on the table. Quietly, he knocked on Misato's door. "Breakfast is ready, Misato-san." She came out a minute later, yawning as she brushed away a stray strand of her hair. Walking out, they were both surprised when the doorbell rang. Shinji rushed to answer the door.

There, standing with a smile, was his father, Gendo Ikari.

"Hello, Shinji."

"Father!" He cried out, startled. "Is there something wrong?"

"No, it is fine. I just wanted to visit you. If I had disturbed you, then I shall go."

"Oh, oh of course not! Come in father!" He felt something stirring inside him. Why? "I'm sorry I didn't know you were coming. There's still some extras from the rice rolls that I was making. Would you like them?"

 _What am I doing? Why am I…. am I trying to please my father? Why would I want to do that?_

Gendo smiled warmly, something he didn't realise was possible. Misato blinked a few times, then realised who it was there. "Oh ohayo Commander Ikari," she says. "I'm sorry I didn't expect you."

"It's fine, it's fine. Shall we eat then? I think Shinji made rice rolls." "Sure, and would you like a can of beer?"

And so easily was the tension in the air released, the three of them talking and laughing through the morning, it felt like a family. Not that the 'parents' were interested in each other, but they were truly the ones who can be a parent for Shinji. He never thought that coming to Tokyo-3 can bring such a change. Before, when he hadn't came, he was alone. But now his father accepted him. He found a mother in Misato Katsuragi. He has a family. There are those who love him. He turned toward his father, wondering what's on his mind. But inside the mysterious mind of Gendo Ikari, there was one interesting thought.

 _Just wait till you meet Naoko. She is such a kind person. I miss her so much, and just maybe… I love her more than your mother._

After they were done with breakfast, Misato volunteered to wash the dishes, saying to give the two some 'father son bonding time', leaving the two in the kitchen. There was a moment of silence, before Gendo spoke. "Do you remember your mother, Shinji?" He gasped, not thinking that his father would bring this up.

"No-I was too young then, I didn't really realise what happened. I don't have any photos either."

Gendo smiled with regret. From his coat pocket, he pulled out a photo, kept clean and unstained carefully throughout the years. "Here." Shinji immediately let out a cry in shock. "Isn't that… Ayanami?" Why does she look so much like mother? "That is your mother. And yet, Ayanami is something else. Do you want to know the truth? You may not like it, and instead want to hold on to the perfect image of your mother, but it is best if you know the truth. Lies can kill."

He was confused. Was mother not like how he thought? Did he really see her in Unit 01? But here was father, actually reaching out to him in a way he never thought possible. When he thought no one cared.

"I will know of the truth then." He said. "I don't want to be fed lies."

"Then come with me." Gendo smiled sincerely, proud that his son would make such a choice. That he would accept the unknown. "I'll take you to Central Dogma."

At his own apartment, the albino boy frowned slightly. "So you will be coming, along with the chairman, after Ramiel?"

"That is correct," a soft female voice said on the other end. "I look forward to seeing you, brother."

"The same goes for you, Sister." He smiled once more, remembering their plan. "I believe all will be well."

"If so, goodnight."

"Wait," He says. "Tadhiel?"

"What is it?"

"Stay safe." He did not understand why he said it, but somehow it felt right.

"Of course, Tabris." She hung up then, and he gave a slight sigh of relief. It was much easier to have someone share your burden, to not be alone. He gazed out at the stars, reminiscing the past. The secrets that he could never share. Rei's smile entered his mind. He owed her the truth. He'll tell her. One day.

(A/N): Well who is this mysterious girl on the phone with Kaworu? OC, but who do you think she is? Review if you can!


	6. Chapter 6

Chapter six: Truth act ll

Shinji followed his father to Nerv, along with Misato, who insisted on coming. They entered the elevator silently, each feeling the lack of the need to speak. The silence was unnerving, yet none of them could think of anything to talk about, as this occasion felt ceremonial. He clenched his fists. He would not run away now. There would not be any turning back. He must know the truth for himself. Even if he wouldn't like it.

 _I must become stronger._

He gazed at his father, then Misato, both with hard eyes. They looked so different from before now. How strange, that a person can have so many sides to them. The cold white light of the elevator suddenly turned off, and the elevator came to a jolt. He let out a cry at the sudden stop. They were trapped.

"Well, it seems like someone doesn't want you to know." Gendo said with a smirk. With his bare hands and Shinji's help, they wrenched open the elevator door. They were greeted by Unit 01's menacing green eye.

"Hello, Yui." Gendo greeted casually, "What are you planning?"

Unit 01's hand grabbed all of them, and rose back to the surface. Letting them down on the geofront, she gave one last glare at Gendo before taking her leave.

"So she isn't willing to let me show you two until the appointed time after all," Gendo muttered. "How irritating. Though this proves that your mother's intentions aren't all that benign, doesn't it?" Shinji nodded slowly, still trying to comprehend what just happened. What was mother trying to do? He turned his head, and to their surprise, Rei and Kaworu walked over.

"How are you, Rei?" The commander smiled at her warmly. "All is going well, Commander," she answered. "We just had a sync test. Our scores have improved slightly."

"That's great, Rei!" Said Misato excitedly. "You'll have to work hard too, Shinji-kun." He nodded once more, but a smile formed on his face. I do belong here.

"So what activities have you been indulging in, Ayanami-san?" Shinji asked curiously.

"I have been spending time with Nagisa-kun," she said, bringing attention to the silent boy, whose smile seemed to penetrate through everyone's defenses. "He is very kind to me," she added with a slight blush to her cheeks.

"It seems to me there is quite a gathering here," a voice came from behind them. It was Ritsuko. "Shall we all have lunch together?"

Behind her, Gendo Ikari considered his options. On one hand, he could foster a sibling relationship between Rei and Shinji, and bring everyone together. But on the other hand, Seele's pilot was here, and he cannot discuss with Ritsuko about certain circumstances.

"Seize the opportunity whenever you can," Yui's face formed in his mind. "There is much to learn from every interaction."

Very well, then. He thought to himself. "That is nice. We can also get the pilots acquainted. Let us have lunch, then."

He did not miss the boy's red eyes on him. He has much to learn from him.

 _I will use everything you taught me, Yui, and defeat you with it._

At the cafeteria, everyone took a seat. Gendo did not miss Kaworu and Rei holding hands, and that glow in their eyes. Ritsuko and Misato discusses about the children's sync ratio casually, and something about the fourth child having an accident. No matter, he will ask the committee about that later. Shinji stares down at his food, somewhat hesitant.

"Is there something wrong, Shinji?" He asks, unsure if this is how he should phrase it.

"Nothing… it's just that I've never had a meal with so many people before. I'm just not used to it." Shinji looks up, then smiles. "Well then, I'll eat!"

As Shinji chats with Misato casually, Ritsuko moves next to him, and whispers into his ear. "Rei's sync ratio increased again. It's a good sign, probably due to Kaworu. When's my mother going to arrive?"

"Soon. They're already arranging it. Unit 02 and its pilot will come afterwards. It's too bad that there was an accident with Unit Alpha. However, they say there's actually a chance that the pilot may live. We are still awaiting news on their end."

"I see. We are really sinking deeper in this path… we mustn't let Yui's plan come to fruition. Even if it ends up with the worst case scenario, we need to have Shinji prepared, so that he will not need instrumentality."

"How's the tests on Sachiel's carcass going?" "Pretty fine. We discovered that their dna is quite similar to ours. 99.99% actually. Not very surprising considering the truth of everything."

"I guess so."

Ritsuko then goes on eating, and he takes bites out of his own also. Kaworu seems to be whispering urgent words to Rei, who nods slowly. The two then shares a knowing smile, their words unheard by everyone. Gendo Ikari wonders at this. He never realised how the Angelic children are able to love. Perhaps, it was that he never spent much time with Rei, having too many memories of the dark past, or was it that she so resembles Yui that it becomes unbearable, almost as if she is watching him now? All he knows, is that if he fails, there shall be no mercy.

Not for him, not for Naoko, not for Yui, not for Ritsuko, not for the children, and certainly not for mankind.


	7. Chapter 7

Second Chance: chapter seven

Melancholy

Shinji found no trouble putting on his new school uniform. It was not much different from his usual attire, comprising of a simple white shirt and black trousers. Putting his computer into his bag, he walked out the door.

"I'm leaving," he said, though not expecting an answer. "Misato-san, there's still some instant curry in the fridge. Save it for yourself."

"Mmmmmmphhhhh" her reply came, muffled and unheard.

Shinji sighed, then began walking to his school. Father had told him that the other pilots will be there, in the same class as him. Class 2A. He wondered about school.

"Ikari-kun."

Shinji turned around, and saw Rei standing there. To his surprised, she was alone.

"Um... Ayanami?" He asked, hesitant. "I thought you would go to school with Nagisa-san."

"He is unwell today," Rei turned away slightly. "Do not question this anymore. I would like to introduce you to the school campus. Follow me."

Shinji contemplated his options for a moment, before following her, quickening his steps. "So, uh, how long have you been piloting?"

"Seven months," she answered. "What is the reason for this inquiry?"

"Nothing," Shinji muttered quickly. "I hope your injuries heal soon."

"They will not impede my ability to pilot," she said. "Besides, we have arrived."

Rei led him to their room. Rei took a seat beside the window, and just before he could take the seat beside hers, she stared at him.

"That's his seat. Please sit in the empty seat behind me."

"Oh, oh I'm sorry." He apologised, feeling rather disturbed by her coldness. "I'll sit there then."

"You're making the new student nervous, Ayanami," the class rep scolded lightly. "You must be Shinji," she smiled at him. "Welcome to Tokyo-3 middle school. You may use your computer int the lesson if you are not too loud."

"Sure," Shinji replied. He unpacked his things, and found himself staring at the still back of Ayanami's head, her blue hair incomprehensible to him.

 _Why is she so cold to me?_

The lessons flew by. It was monotonous, as Shinji guessed that what the sensei taught was a cover-up story. He tried to understand Ayanami, but found it impossible. She was so warm the other day, how is it that she seemed to dislike him so much now?

"Stand! Bow! Sit!"

The bell rang, and school was over. Shinji packed his things and prepared to leave, but not before a hand landed on his shoulder.

"Hey, how is it that Ayanami hangs out with ya? She's like, the ice queen except to Nagisa. Those two are almost suffocating to look at." An athletic boy with dark skin said.

"Well, we're both pilots..." Shinji hesitated, but before he could finish, he was interrupted by the gasp of the whole class.

"Were you the one who piloted that giant purple robot that day? That's so cool!" A boy with freckles and glasses said.

"I thought only Ayanami piloted!"

"But no newbie could have fought like that! That was so skilled!"

"Um.. it was Nagisa-san's work, really." Shinji protested.

"Uh, so it's still those freaks eh?"

"Can't be anyone else."

"Wish it was this kid, though. Ayanami and Nagisa just feels wrong to me. I mean, even this kid is more normal. He would be so much better."

Shinji walked away quietly, not wanting to hear more of it. From what he knew, Ayanami and Nagisa were both rather nice people. Why would the others hate them so much though? What had they done?

From the corner of his eye, he saw Rei watching him.

 _I'm sorry, Ayanami, but I'm not strong enough..._

He realised why she was so cold to him though.

Probably no one in school gave her and Nagisa credit for what they did.

"How was school, Rei?" He smiled, floating in the tube of LCL. "I heard Shinji-kun went too."

"It was as usual." She said, turning away. "I dislike how you always speak of him, Nagisa-kun."

"That's a very human feeling," he laughed a little, bubbles forming from his mouth. "But don't worry, I won't leave you behind."

"What if you do?" She asked. "You always say you will tell me why you always speak of him. Yet you have not done so."

He sighed, the LCL draining out of the tube. "I am waiting for my sister. It will be easier to explain then."

He stepped out of the tank, and casually tossed her a glance that she understood immediately. _Meet me at night._

"I think the next Angel with arrive... very, very soon. I will fight in your place."

He then left, leaving her alone in the room, staring at the clones.

 _You have been my only hope, the only one who understood, despite that the members of Nerv are kind to me... th_ _ey are human. And if you lay eyes for another, what will I do?_

 _I need you._


	8. Chapter 8

Chapter Eight

Startling breakthrough

Shinji walks through the corridors of Nerv, having finished another sync test. He was told that his score has risen by a little.

Dr Akagi Ritsuko tells him that Unit 00 has completely been repaired, and will also be deployed in the next battle. However, since Rei's injuries haven't completely healed, it will be Kaworu fighting.

He muses over that. Nagisa-San seems quite an interesting person. Rei likes him, Dr Ritsuko cares about him, his father doesn't seem to trust him, his classmates hate him. Maybe he should ask why. But then, that may seem impolite indeed.

Deep in his thoughts, he did not see the older woman rushing from the corridor. He crashed into her, causing her to fall.

"Oh, I'm so sorry," he apologises quickly, helping her back up. "Are you alright?"

"I'm fine, don't worry." She smiles at him. "You must be Shinji-kun. It seems like you have grown up fine. I hope Gendo treated you well."

"Um… Who are you and how do you know my name?"

"Well, it has been a pleasure to meet you, but I must go see my daughter first. Let's leave the introductions for later!"

Carrying the heavy pile of files, she walks away. A few moments later, Dr Ritsuko's voice could be heard echoing through the hallways.

"MOTHER!"

"Welcome back, Akagi-san." He walks in.

"Oh, it's good to see you also, Kaworu."

"I hope that you are feeling better. The after effects of what I can do are not very pleasant."

"It's alright. How's Rei?"

"Pretty good," Ritsuko cuts in. "The new system is better than what Yui did. She doesn't need medication as frequently anymore. Now, mother, explain. They said you went into a coma. You were brought back because you were supposed to be dying. What. did. you. do."

"Well…" Naoko smiles. "I dreamed. With help of Kaworu-kun's A.T. Field I entered into a sleep within my subconscious which helped me discover the origins of mankind and also figure out certain things about Eva and Angels. He keeps me up to date with what's happening, and I help him find a way to resist the urge of the beginning."

"Wait." Ritsuko shakes her head. "I don't understand what you are talking about. How does he have an A.T. Field? What is the urge of the beginning? All those years I was worried, and you were dreaming?"

Naoko and Kaworu stares at each other.

"You didn't tell her?" They say in sync.

Ritsuko sighs.

"Well, Yui's not going to be happy." A new voice adds.

"Gendo, you old man." Naoko says. "Took you so long."

"I am the commander of Nerv. I have matters to deal with. Besides, how did you even escape the hospital room?"

All eyes on her, she smirks.

"I slammed whatever medication they gave me into everyone in my way. I then ran from a giant robot chasing after me in jealousy. Then, as she was chasing, I crashed into Shinji-kun, making it impossible for her to chase after me anymore. You better start repairs and hospitalisation for all involved."

"You were given very, very heavy sedatives."

"Then it's your job! You're the commander, you said so yourself. Go clean up."

Gendo sighs. Naoko's even harder than Yui.

Shinji walks on, heading to the cafeteria. That was a strange encounter.

To his surprise, Rei walks in, and buys a drink. She walks straight up to him, without pausing.

He takes a step backward, shocked.

"Um...what are you doing, Ayanami-san?"

"Here." She hands him the drink, and leaves.

Shinji stares at the drink. Taped to the top, is a tiny hard disc.

In Nerv Berlin, Germany, in a hospital, a girl makes a phone call.

Kaworu picks up his phone.

"Brother, Keel will be coming after Ramiel in a VTOL. With only me. Prepare explosives by then.

Also, Shamshel is coming. That is all. GoodBye."

There is a moment of silence.

"You all heard it, didn't you." He sighs.

"You have a strange sister."

"Your sister is alive?"

"Yes and yes…" he turns away. "But I guess we'll all have to leave this discussion for later. Shamshel is coming."

The three of the, walks out of the office. Kaworu goes to change into his plugsuit, while the two scientists direct the preparation for the Evas.

He sees Rei, walking towards him. He shakes his head.

 _I can't let you bear that pain._

*omake*(this does happen in the story, though)

Faraway, the girl makes another call.

Keel Lorenz sighs. He ponders for a moment. He picks up the phone.

"Screw you."

Keel Lorenz sighs. That cost.

(A/N): Yes, you will see more and more of my OC. She is NOT a self-insert. She is my muse.


	9. Chapter 9

Chapter 9: Fiery Battle

Shinji Ikari breathed deeply. He leaned backwards, heaving, allowing the LCL to soak into his lungs. He placed his hands on the controls, and sunk into the warmth of the plug.

There was a smell, so familiar. Was it mother? He couldn't trust her, surely, after what his father told him. But he was sure he will be protected. She would be with him.

A screen opened up on the side. 'Are you ready, Shinji-kun?' Misato asked him. 'The progressive knife is in the shoulder pylons. You will have five minutes of battery if you lose the umbilical cable. Nagisa will engage the Angel first. You simply have to enter the fray if any error occurs. Are you all clear?'

He nodded, his eyebrows tightening. He let out a breath he did not know he held as the Eva rose through the shaft. He stepped forward, dragging the umbilical cord behind him. From the distance, Eva Zerogouki rose, with a Progressive knife in hand, ready for battle.

He sighed. He would have to wait. His mind was still on the hard drive given to him by Rei Ayanami.

Nagisa Kaworu was confident that he, both as a pilot, and an Angel, could surely defeat Shamshel. However, he knew that the soul within this Unit found him alien, different, intrusive. So cautious he was, holding the Progressive knife, as he crept behind the trees, hidden from the other Angel.

The soul probed, searching. _Who are you,_ she asked. _Why are you here? Why not her?_

He did not respond. Surely if she looked deeper, she would find the answer, clear though unspoken. Shamshel was his priority now. He shook his head. Thoughts of the night he spent with Rei remained in his mind. They watched the stars glide across the sky, by the hillside, finding peace within themselves doing that.

 _I see._ She said, warmly. _You like her. But only with me is she whole. I will aid you._

A surge of strength went through him. He raised his sync rate a little, not too obviously. The soul in Zerogouki and he had a single wish now.

 _Protect Rei._

Without hesitation, he ran. Throwing off the umbilical cable, the timer started counting down, 05:00. He held his progressive knife before him, rushing towards Shamshel at the speed of light. The Angel turned, with mild surprise, and sent its whips of light towards him. He jumped away, out of reach, before making a leap onto Shamshel's head. Taking his progressive knife, he tried to cut away the A.T. field, but was not given the chance before another of its whips threw him off, several hundred metres away.

He looked at the timer— only two minutes left. It was too far away to grab the umbilical cable now, and he knew he did not have enough in himself to push this Evangelion to berserk mode. Just then, Evangelion Shogouki ran out, the umbilical cable dragging out behind it. His eyes widened. This was not in his plan.

"Shinji-kun, get back!" He cried out.

But he was not heard. Shinji rushed at the Angel, his mother's soul with him. This was his chance. He had to prove to his father that he was worth it all. If he had to pilot the Evangelion, he would do it. He would do anything, as long as his father cared about him. His heart pulsed furiously, as he found himself shaking. He was so very afraid, but he could not falter.

It was not long before he threw off his umbilical cable also, which Kaworu attached to his own Evangelion. Shogouki spread its A.T. Field, blocking the whips of light.

 _Mother,_ Shinji whispered. _Please protect me as you always have._

He abandoned all caution and gave a beastly roar, tossing his progressive knife at the Angel's core while trying to grab at the the whips. It would go well. This was where his worth lay. His father would always be with him. He would trust him—

And then the A.T. Field of Evangelion Shogouki faltered.

The whips of light soared through the air, cracking and glowing, as he braced himself for the blow. _Why?_ He cried out inwardly. _Why did his mother abandon him?_

It never came. Standing in front of him, pierced through by two glowing tendrils, was Zerogouki. Shinji watched in horror. What had happened?

"You fool," Nagisa raised his eyebrows. "That is why I couldn't let you get in the way. Take the umbilical cable, I will finish off the rest."

Shinji complied as he watched him pull the tendrils even closer to himself, despite wincing through the pain. The Evangelion inched closer and closer to the Angel, so close they could be in an embrace, before it collapsed onto the Angel. Zerogouki's timer had sounded. He had ran out.

But the Angel was held in place, unable to move. Shinji moved forward, careful not to break the umbilical cable. He had to reach it. The progressive knife lay just a little further before him. He would not fail. Even if his mother would not support him, he still had to win.

He didn't need to. A red Evangelion soared down from the sky triumphantly, like a Phoenix. It had four green eyes, and held a progressive sword in its hand. A jetpack kept the Evangelion in flight, spinning in the skies.

"Sorry I'm late!" A girl's voice sounded out loudly. "I'll finish it up!"

The red Evangelion landed swiftly, and cleanly removed the tendrils. Pointing her sword towards the sky, she cried out, "ERSTE!"

The sword went down and cut through the Angel's core, as Shinji watched on, amazed yet disappointed. How could he compare to someone like that? That exuberant attitude without fear, when he himself was always afraid. What was he now, if he couldn't beat a single angel on his own?

The three Evangelions all ejected their plugs, waiting for rescue. In his own, Nagisa Kaworu smiled.

"Now this is going according to plan," he narrowed his eyes. "The second child, Asuka Langley Soryu, has arrived."


	10. Chapter 10

Second Chance

Chapter ten: Aftermath

()

The three pilots, Misato and Ritsuko stood before Commander Ikari Gendo at his office.

"I am glad to see the Angel destroyed. Was much damage done to the city?" He asked.

"Little, Commander. We can surely finish repairs in a month's time." Misato answered, standing tall in her uniform.

"How are you pilots?"

"We did not take much damage and I was injured only slightly." Kaworu replied.

 _Slightly injured,_ Gendo mused. _As if. Normal people don't heal from feeling like getting pierced by two whips that quickly. And you even pulled them towards yourself._

"That is well." He responded audibly, hiding his thoughts. "You two?"

"It wasn't too bad for my debut!" Said the red haired girl-Asuka, he remembered her name.

He wondered if such a cheerful girl was a good addition.

"Um..." Shinji hesitated.

"I'm sorry I couldn't defeat it. I should have done better."

Shinji looked down, unable to meet his father's eyes. He didn't want to see the disappointed look that was surely on his father's face.

Gendo sighed inwardly. He himself should have done better at raising his son.

"You did well, Shinji." Gendo spoke suddenly. "Same goes for the others."

Shinji blinked. _He praised me._

"What about the Evas? Have they sustained much damage?" He continued.

"It is all within the budget. Nothing we can't handle." _And will save us another troublesome meeting with Seele,_ Naoko finished silently.

"With all due respect, we should get on with the work." Ritsuko added.

"Very well, you're all dismissed." Gendo finished finally.

Had anyone looked carefully, they would have seen a small smile on Shinji's face as he walked out.

()

"So, are you two the only pilots here?" Asuka asked, munching on a sandwich as the three pilots sat in the cafeteria. "You," she pointed at Shinji, "seem a little too glum, and you," she pointed at Kaworu, "kept smiling for no good reason. You people here are weird."

"There is one more pilot, and she's the one who actually pilots Unit 00." Shinji answered. "Oh, Ayanami, I didn't realised you came."

Asuka turned her head and stared at the bluenette for a moment. And a smile came to her face.

"Ooh, finally another girl! Nice to meet you, I'm Asuka." She stretched out a hand.

Rei stared at the outstretched hand for a moment. Hesitantly she took it.

"I am Rei. Ayanami Rei." _I am me._ "Are you injured from the last battle?" She asked, slight concern appearing in her features.

"Shamshel got me." Kaworu laughed.

"Angels have names?" Shinji asked.

There was a moment of silence as Rei and Kaworu gazed at each other, some unspoken conversation taking place between them.

"Nicknames." Rei said simply.

"Well, anyways, it's great to meet you all! And really, are all the clothes you have school uniforms? I have to take you all out shopping. You'll all become a different person with my professional touch. No more wearing uniforms on holidays."

This time, all three of them gazed at her hesitantly.

"What?" She asked. "Anta Baka? My acquaintances can't dress like that. If you're to be my friends, we have to go and have fun together!"

 _She's weird._ All three of them thought.

 _But not necessarily a bad comrade to have._

()

"How's everything going, Rits?" Misato asked. "Have a cup of coffee." She passed her a cup, to which Ritsuko gave a quick nod of thanks.

"And stop smoking, daughter. I already let you off for dying your hair, but your health is important." Naoko added.

"Can't!" Ritsuko spluttered, in between gulps of coffee. "Can't work if my hands shake. And Misato, even Rei makes better coffee than you do."

Misato huffed. "I don't usually demand such high quality stuff! I just drink UCC!"

"Anyways, the real issue is, Unit 02 feels a little weird to me. An Evangelion needs a soul to work. Both Asuka's parents are alive, and she doesn't have any siblings. So I have no idea how she's able to synchronise with her at all."

"She hasn't shown any use of the A.T. Field yet, so there are still possibilities..." Misato attempted.

"But theoretically, she should not be able to move the Eva. At all." Naoko countered.

"But shouldn't you be able to sense whether there's a soul in it or not?" Misato asked. "I've heard a bit of rumours about Unit 01, and Unit 00 is a prototype, so there should be some information on this one."

"Magi is unsure." Naoko answered once more. "You should rest, Katsuragi-san. Rits-chan and I will handle everything here."

Misato gave one last glance, before leaving the platform.

As soon as she was out of earshot, Naoko whispered in Ritsuko's ear. "Are you sure this is accurate? We can't just trust the Magi on everything, even if I made it."

"Yes," Ritsuko replied gravely. "And part of my guts say so too. I have to say unfortunately, there may be fragments..."

()

Asuka walked out of Nerv, humming a tune beneath her breath. There was a skip in her step as she remembered her victory, defeating the Angel. She was worthy, after all. She was the right person for this. This was where she belonged.

 _Everything's gonna be alright, where there are friends, even if papa and mama wouldn't come with me..._

 _All's right with the world._

()

(A/N): So finally, here comes the great Asuka Langley Soryu. I wanted to get her sooner, since it would be useful, and I got tired of waiting for myself to finished all the chapters between the Angel attacks. She's friendly, she's happy, but this is Eva, so there will be reasons.

Oh, and tell me if you want to meet my Oc or not. If you don't, I'll consider deleting her out of the story.


End file.
